Author: Reeder, Jens; Steffen, Peter; Giegerich, Robert
Title: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Document date: 2007_5_3
ID: zgv4kd6j_7
Snippet: Our first extension is the capability to compute nearoptimal structures. Often the native structure of an RNA is not predicted as the MFE structure. This may stem from uncertainties in the energy parameters, or the molecule may not reach its MFE structure, either due to interactions with another molecule or by ending in a kinetic trap. In such a situation, alternative near-optimal structures may be better predictions. All methods of pknotsRG can .....
Document: Our first extension is the capability to compute nearoptimal structures. Often the native structure of an RNA is not predicted as the MFE structure. This may stem from uncertainties in the energy parameters, or the molecule may not reach its MFE structure, either due to interactions with another molecule or by ending in a kinetic trap. In such a situation, alternative near-optimal structures may be better predictions. All methods of pknotsRG can now be run in a suboptimal mode, where all suboptimal solutions up to a user-defined threshold are computed. This is done in a way similar to RNAsubopt (9) from the Vienna RNA package for pseudoknot-free structures.
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